Thursday, 31 May 2012

Additional shots of the BGI meeting in our University

The roundtable with some professors of University of Brescia and the "delegacy" of BGI Europe.
Here Dr. Ning Li (Ceo at BGI europe) is drawing our attention on the crucial issue of data analysis in NGS.

"Technical strategy at BGI" a slide from the talk "Genetic testing at BGI Healthcare" by Miss Hui Jiang. (Deputy Director of Technology Development at BGI Europe)

The BGI team, probably the average age is 33 (...or less).

A summary of the number of NGS platforms around the world: try to bet who is the winner...

The meeting is finished but the topics to discuss are many.

P.S. Sadly during the meeting Northern Italy was shocked by two strong hearthquakes (and we felt them), 11 persons died that day in Emilia Romagna area and our thoughts are with them.

Tuesday, 29 May 2012

Lets BGI inspire your research!

May 29th, BGI@Brescia.

This morning we had an exciting meeting with BGI staff to explore the possibility of establishing collaborations with this sequencing juggernaut.
The 7 members of the BGI arranged 4 presentations covering their main activity in generic whole genome sequencing, single cell sequencing in tumors, use of NGS in diagnostic applications and in GWAS studies. Of course their potential and their expertise on NGS technology goes far beyond our present little expertise in the field, but we are sure that this meeting demonstrated to everyone the wide range of fascinating and powerful approaches based on the new sequencing techniques. Lets BGI inspire your research!

Meanwhile take a look to this short video showing part of the presentation made by Dr Yong Hou (Director, Research Institute, BGI Europe; Head, Single Cell Analysis Group, R&D, BGI, Shenzhen; Head, Lab. of Genome Structure and Function, R&D, BGI, Shenzhen) on sequencing applications for tumor studies and single cell sequencing.

Live from Aula consigliare: BGI is ready to start

Sunday, 27 May 2012

BGI Workshop at the University of Brescia

Sometimes the mountain goes to Mohammed. This Tuesday, the 29th of May, scientists and representatives of BGI will present their services and scientific projects in a workshop entitled "Impact of breaking genomic techniques into disease diagnosis and mechanisms". The workshop will take place in the Aula Consigliare of the Faculty of Medicine, University of Brescia starting from 9.00. The meeting has been organized by the Department of Biomedical Sciences and Biotechnology. A more detailed program of the event is available at this link.

Monday, 14 May 2012

CGHub at UCSC: Cancer data at Petabyte scale

Recently there were several announcements about genomic data made available on the net, supporting the idea of a new era in genomics when data production greatly exceed data analysis capacity. So the solution is to make all these data avaiable to the community and let other research groups to continue the analysis. The recent CGHub initiative from UCSC and NCI goes exactly in this direction and stands out for the dimension of the dataset.

Indeed, University of California Santa Cruz, that everybody knows for its famous Genome Browser, is now building a petabyte-scale data repository for cancer genome projects, called CGHub (Cancer Genomics Hub).
The project is funded by the National Cancer Institute with over $10M and it started with 5 petabytes avaiable and the possibility to growth as needed by the three main NCI cancer genome projects: the Cancer Genome Atlas (TCGA); the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and the Cancer Genome Characterization Initiative (CGCI).
Therefore, CGHub will soon become the largest available dataset on cancer genomics ranging from adult cancer to childhood cancer to HIV-related tumors.

Currently, TCGA alone generates about 10 terabytes of data each month and its output is expected to increase rapidly getting to a total amount of 10 petabytes of DNA and RNA data from the 10,000 patients involved.
Besides providing the space, UCSC is also working on innovative software solutions to grant rapid and flexible access to this huge amount of data, as well as to compress them and simplfy the management of a petabyte scale storage.
"We would like to compress the data down to one tenth of its current size and that will not be possible without losing some information," told David Haussler, a professor of biomolecular engineering at UCSC in charge for the CGHub project. At present, the cancer genomics community is "working very hard to decide what information we can sacrifice in these very valuable data."
More information can be found on this post from GenomeWeb Bioinform and on the offical pages of TCGA, TARGET and CGCI.

Friday, 11 May 2012

Flash Report: Life Technologies official reply to Loman's paper

Life Technologies has posted a reply to the "Performance comparison of benchtop high-throughput sequencing platforms" manuscript published in April on Nature Biotechnology.
Here is what they did:

How did we address some of the challenges?

• We obtained a sample of the EHEC E. coli isolate, the week after the paper was released
• We sequenced this sample using up-to-date Ion sequencing kits and software
• We directly compared the data from Loman et al July 2011 to Ion publicly released data from May 2012*
• We aligned the reads using the genome sequenced in Loman et al to measure accuracy
• We performed de novo assembly to measure how well the PGM performs for this application

Using the most recent chemistries, algorithms and the 318 Chip, the Ion Torrent PGM error rates are definitely lower (the majority of bases are Q30 or better), although in this area the MiSeq seems to have an edge on the competition, particularly in the homopolymer stretches.
It is however remarkable that in 9 months (July 2011 - April 2012) the indel and homopolymer accuracy has improved ~450% on the Ion Torrent platform.

Thursday, 10 May 2012

Genome vs Enviroment: the twin match.

"What fraction of the population would benefit from genome sequencing? “Benefit” in this context is defined as receiving information indicating that the risk of disease is increased or decreased to a degree that would alter an individual's lifestyle or medical management." This is the starting question that Roberts et al. wanted to answer to. Right now this seems an unsuccessfully effort, an impossible challange given the millions of variants that could contribute to the risk of a disease. However there is a field in which this challenge becomes easier: the genome of twins. Infact, as the authors wrote in their article published on Science Translational Medicine, in a pair of twins in which at least one is affected by a disease, the probability of the other twin developing a disease is dependent on the genome whenever that disease has some genetic component. The study was conducted on 53,666 twin pairs, analyzing 24 disease. The researchers, given the affected status of one of the two twins, used the prevalence of the disease in the second twin to calculate the genetic risk of a given disease for that genome. The results, elaborated without any type of sequencing effort, reveal that the majority of the twins would have tested negative for risk for 23 of the 24 diseases, substantially their risk was below the risk of the general population. This article received many critical comments, here you can find a series of them posted on the Nature blog, the main critics focused on the low novelty of the study. It is well known that twins could get sick of different diseases and also die for different causes that don't depend on their common genome.
What emerges from this work is that our genome, and its whole sequencing, is valuable and instrumental for the identification of the basis of many genetic disease, primarily for those with a family history. On the other hand, enviroment has the main role in many medical conditions, especially in complex diseases such as cancer. This is not a bad news because, indipendently of our genetic starting conditions, the match against complex diseases is open, and weapons such as diet, sports, and lifestyle, could make us the winners.